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TCGA2STAT specifications


Unique identifier OMICS_10650
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
parallel, knitr, CNTools, XML, R(≥3.0.0)
Maintained Yes


No version available



  • person_outline Ying-Wooi Wan

Publication for TCGA2STAT

TCGA2STAT citations


Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub classification

PLoS Comput Biol
PMCID: 5839591
PMID: 29470520
DOI: 10.1371/journal.pcbi.1006026
call_split See protocol

[…] We downloaded TCGA data from the TCGA data matrix on November 30, 2015 using the TCGA2STAT R package []; This gave us a total of 34 RNAseq expression datasets with their adjoining survival and clinical information. We used the level 3 data normalized using RSEM. We used the datase […]


Improved high dimensional prediction with Random Forests by the use of co data

BMC Bioinformatics
PMCID: 5745983
PMID: 29281963
DOI: 10.1186/s12859-017-1993-1

[…] A RNASeqv2 profiles of head-and-neck squamous cell carcinomas (HNSCC), which were downloaded together with the matching normalized DNA copy number co-data from Broad GDAC Firehose using the R package TCGA2STAT. Of the 279 patients described in [], we used the subset of 133 patients that had HPV-negative tumors in the oral cavity. Of these patients, 76 presented a LNM and 57 did not.To enhance the […]


Villi specific Gene Expression Reveals Novel Prognostic Biomarkers in Multiple Human Cancers

PMCID: 5604211
PMID: 28928868
DOI: 10.7150/jca.19787

[…] We used the R package “TCGA2STAT” to download the RNA-Seq data and clinical data of patients representing 32 cancer types from The Cancer Genome Atlas (TCGA) database. For RNA-Seq data, we downloaded the RNAseqV2 data for e […]


A novel signature for stratifying the molecular heterogeneity of the tissue infiltrating T cell receptor repertoire reflects gastric cancer prognosis

Sci Rep
PMCID: 5552765
PMID: 28798410
DOI: 10.1038/s41598-017-08289-z

[…] the log-rank test using the R package “survival”. The RNA-seq data and corresponding clinical information, which were available for 388 GC samples, were downloaded from TCGA database using R Package “TCGA2STAT”. […]


Integrated transcriptomic analysis of distance related field cancerization in rectal cancer patients

PMCID: 5617410
PMID: 28977850
DOI: 10.18632/oncotarget.17864

[…] TCGA CRC RNA sequencing data used for the survival analysis were accessed using the R package “TCGA2STAT” []. We calculated 5-year overall survival for the 7-gene signature and for each single gene using data from the TCGA CRC dataset. Hierarchical clustering of the expression of the 7 genes di […]


Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non coding RNA signature of fibrolamellar carcinoma

Sci Rep
PMCID: 5356346
PMID: 28304380
DOI: 10.1038/srep44653

[…] tal and from the Cancer Digital Slide Archive. Liver histology was reviewed independently by two gastrointestinal pathologists (KGG, MST). Ages of patients were obtained from TCGA using the R package TCGA2STAT. […]


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TCGA2STAT institution(s)
Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA

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